Trac #22047: Scipy fails to build with ATLAS

If Sage is configured with `./configure --with-blas=atlas`, then `scipy`
fails to build:
{{{
[scipy-0.17.1.p0] Found local metadata for scipy-0.17.1.p0
[scipy-0.17.1.p0] Using cached file /usr/local/src/sage-
git/upstream/scipy-0.17.1.tar.gz
[scipy-0.17.1.p0] scipy-0.17.1.p0
[scipy-0.17.1.p0] ====================================================
[scipy-0.17.1.p0] Setting up build directory for scipy-0.17.1.p0
[scipy-0.17.1.p0] Finished extraction
[scipy-0.17.1.p0] No patch files found in ../patches
[scipy-0.17.1.p0] ****************************************************
[scipy-0.17.1.p0] Host system:
[scipy-0.17.1.p0] Linux tamiyo 3.17.7-gentoo #1 SMP PREEMPT Wed Dec 31
20:06:39 CET 2014 x86_64 Intel(R) Core(TM) i7-2640M CPU @ 2.80GHz
GenuineIntel GNU/Linux
[scipy-0.17.1.p0] ****************************************************
[scipy-0.17.1.p0] C compiler: gcc
[scipy-0.17.1.p0] C compiler version:
[scipy-0.17.1.p0] Using built-in specs.
[scipy-0.17.1.p0] COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.9.4/gcc
[scipy-0.17.1.p0] COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-
gnu/4.9.4/lto-wrapper
[scipy-0.17.1.p0] Target: x86_64-pc-linux-gnu
[scipy-0.17.1.p0] Configured with: /var/tmp/portage/sys-
devel/gcc-4.9.4/work/gcc-4.9.4/configure --host=x86_64-pc-linux-gnu
--build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-
gnu/gcc-bin/4.9.4 --includedir=/usr/lib/gcc/x86_64-pc-linux-
gnu/4.9.4/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-
gnu/4.9.4 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/man
--infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/info --with-gxx-
include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.4/include/g++-v4
--with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.9.4/python
--enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt
--disable-werror --with-system-zlib --enable-nls --without-included-
gettext --enable-checking=release --with-bugurl=https://bugs.gentoo.org/
--with-pkgversion='Gentoo 4.9.4 p1.0, pie-0.6.4' --enable-libstdcxx-time
--enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-
clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-
altivec --disable-fixed-point --enable-targets=all --disable-libgcj
--enable-libgomp --disable-libmudflap --disable-libssp --disable-
libcilkrts --enable-vtable-verify --enable-libvtv --enable-lto
--without-cloog --enable-libsanitizer
[scipy-0.17.1.p0] Thread model: posix
[scipy-0.17.1.p0] gcc version 4.9.4 (Gentoo 4.9.4 p1.0, pie-0.6.4)
[scipy-0.17.1.p0] ****************************************************
[scipy-0.17.1.p0] Note: CFLAGS, CXXFLAGS and SHAREDFLAGS are taken from
distutils,
[scipy-0.17.1.p0]       so their current settings are ignored.
[scipy-0.17.1.p0] /usr/local/src/sage-
git/local/lib/python/distutils/dist.py:267: UserWarning: Unknown
distribution option: 'install_requires'
[scipy-0.17.1.p0]   warnings.warn(msg)
[scipy-0.17.1.p0] /usr/local/src/sage-
git/local/lib/python/distutils/dist.py:267: UserWarning: Unknown
distribution option: 'setup_requires'
[scipy-0.17.1.p0]   warnings.warn(msg)
[scipy-0.17.1.p0] /usr/local/src/sage-
git/local/lib/python/distutils/dist.py:267: UserWarning: Unknown
distribution option: 'test_suite'
[scipy-0.17.1.p0]   warnings.warn(msg)
[scipy-0.17.1.p0] Installing package scipy using pip
[scipy-0.17.1.p0] Ignoring indexes: https://pypi.python.org/simple
[scipy-0.17.1.p0] Processing /usr/local/src/sage-
git/local/var/tmp/sage/build/scipy-0.17.1.p0/src
[scipy-0.17.1.p0]   Running setup.py (path:/tmp/pip-lnNxdH-
build/setup.py) egg_info for package from file:///usr/local/src/sage-
git/local/var/tmp/sage/build/scipy-0.17.1.p0/src
[scipy-0.17.1.p0]     Running command python setup.py egg_info
[scipy-0.17.1.p0]     running egg_info
[scipy-0.17.1.p0]     creating pip-egg-info/scipy.egg-info
[scipy-0.17.1.p0]     writing pip-egg-info/scipy.egg-info/PKG-INFO
[scipy-0.17.1.p0]     writing top-level names to pip-egg-info/scipy.egg-
info/top_level.txt
[scipy-0.17.1.p0]     writing dependency_links to pip-egg-info/scipy
.egg-info/dependency_links.txt
[scipy-0.17.1.p0]     writing manifest file 'pip-egg-info/scipy.egg-
info/SOURCES.txt'
[scipy-0.17.1.p0]     warning: manifest_maker: standard file '-c' not
found
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     reading manifest file 'pip-egg-info/scipy.egg-
info/SOURCES.txt'
[scipy-0.17.1.p0]     reading manifest template 'MANIFEST.in'
[scipy-0.17.1.p0]     warning: no previously-included files matching
'*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src'
[scipy-0.17.1.p0]     no previously-included directories found matching
'benchmarks/env'
[scipy-0.17.1.p0]     no previously-included directories found matching
'benchmarks/results'
[scipy-0.17.1.p0]     no previously-included directories found matching
'benchmarks/html'
[scipy-0.17.1.p0]     no previously-included directories found matching
'benchmarks/scipy'
[scipy-0.17.1.p0]     no previously-included directories found matching
'scipy/special/tests/data/boost'
[scipy-0.17.1.p0]     no previously-included directories found matching
'scipy/special/tests/data/gsl'
[scipy-0.17.1.p0]     no previously-included directories found matching
'doc/build'
[scipy-0.17.1.p0]     no previously-included directories found matching
'doc/source/generated'
[scipy-0.17.1.p0]     no previously-included directories found matching
'*/__pycache__'
[scipy-0.17.1.p0]     warning: no previously-included files matching
'*~' found anywhere in distribution
[scipy-0.17.1.p0]     warning: no previously-included files matching
'*.bak' found anywhere in distribution
[scipy-0.17.1.p0]     warning: no previously-included files matching
'*.swp' found anywhere in distribution
[scipy-0.17.1.p0]     warning: no previously-included files matching
'*.pyo' found anywhere in distribution
[scipy-0.17.1.p0]     writing manifest file 'pip-egg-info/scipy.egg-
info/SOURCES.txt'
[scipy-0.17.1.p0]   Source in /tmp/pip-lnNxdH-build has version 0.17.1,
which satisfies requirement scipy==0.17.1 from file:///usr/local/src
/sage-git/local/var/tmp/sage/build/scipy-0.17.1.p0/src
[scipy-0.17.1.p0] Installing collected packages: scipy
[scipy-0.17.1.p0]   Running setup.py install for scipy: started
[scipy-0.17.1.p0]     Running command /usr/local/src/sage-
git/local/bin/python -u -c "import setuptools, tokenize;__file__='/tmp
/pip-lnNxdH-build/setup.py';exec(compile(getattr(tokenize, 'open',
open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
install --record /tmp/pip-TjA2nI-record/install-record.txt --single-
version-externally-managed --compile
[scipy-0.17.1.p0]     lapack_opt_info:
[scipy-0.17.1.p0]     openblas_lapack_info:
[scipy-0.17.1.p0]     Disabled openblas_lapack_info: (OPENBLAS is None)
[scipy-0.17.1.p0]       libraries openblas not found in []
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     lapack_mkl_info:
[scipy-0.17.1.p0]     mkl_info:
[scipy-0.17.1.p0]       libraries mkl,vml,guide not found in
['/usr/local/src/sage-git/local/lib', '/usr/local/lib64',
'/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     atlas_3_10_threads_info:
[scipy-0.17.1.p0]     Disabled atlas_3_10_threads_info: (PTATLAS is
None)
[scipy-0.17.1.p0]     <class
'numpy.distutils.system_info.atlas_3_10_threads_info'>
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     atlas_3_10_info:
[scipy-0.17.1.p0]     Disabled atlas_3_10_info: (ATLAS is None)
[scipy-0.17.1.p0]     <class
'numpy.distutils.system_info.atlas_3_10_info'>
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     atlas_threads_info:
[scipy-0.17.1.p0]     Disabled atlas_threads_info: (PTATLAS is None)
[scipy-0.17.1.p0]     <class
'numpy.distutils.system_info.atlas_threads_info'>
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     atlas_info:
[scipy-0.17.1.p0]     Disabled atlas_info: (ATLAS is None)
[scipy-0.17.1.p0]     <class 'numpy.distutils.system_info.atlas_info'>
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     /usr/local/src/sage-git/local/lib/python2.7/site-
packages/numpy/distutils/system_info.py:1548: UserWarning:
[scipy-0.17.1.p0]         Atlas (http://math-atlas.sourceforge.net/)
libraries not found.
[scipy-0.17.1.p0]         Directories to search for the libraries can be
specified in the
[scipy-0.17.1.p0]         numpy/distutils/site.cfg file (section
[atlas]) or by setting
[scipy-0.17.1.p0]         the ATLAS environment variable.
[scipy-0.17.1.p0]       warnings.warn(AtlasNotFoundError.__doc__)
[scipy-0.17.1.p0]     lapack_info:
[scipy-0.17.1.p0]       libraries lapack not found in ['', '']
[scipy-0.17.1.p0]     Runtime library lapack was not found. Ignoring
[scipy-0.17.1.p0]       FOUND:
[scipy-0.17.1.p0]         libraries = ['lapack', 'f77blas', 'cblas',
'atlas', 'lapack']
[scipy-0.17.1.p0]         library_dirs = ['/usr/local/src/sage-
git/local/lib']
[scipy-0.17.1.p0]         language = f77
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     blas_info:
[scipy-0.17.1.p0]       libraries cblas,atlas,f77blas,atlas not found in
['/usr/local/src/sage-git/local/lib']
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     /usr/local/src/sage-git/local/lib/python2.7/site-
packages/numpy/distutils/system_info.py:1571: UserWarning:
[scipy-0.17.1.p0]         Blas (http://www.netlib.org/blas/) libraries
not found.
[scipy-0.17.1.p0]         Directories to search for the libraries can be
specified in the
[scipy-0.17.1.p0]         numpy/distutils/site.cfg file (section [blas])
or by setting
[scipy-0.17.1.p0]         the BLAS environment variable.
[scipy-0.17.1.p0]       warnings.warn(BlasNotFoundError.__doc__)
[scipy-0.17.1.p0]     blas_src_info:
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     /usr/local/src/sage-git/local/lib/python2.7/site-
packages/numpy/distutils/system_info.py:1574: UserWarning:
[scipy-0.17.1.p0]         Blas (http://www.netlib.org/blas/) sources not
found.
[scipy-0.17.1.p0]         Directories to search for the sources can be
specified in the
[scipy-0.17.1.p0]         numpy/distutils/site.cfg file (section
[blas_src]) or by setting
[scipy-0.17.1.p0]         the BLAS_SRC environment variable.
[scipy-0.17.1.p0]       warnings.warn(BlasSrcNotFoundError.__doc__)
[scipy-0.17.1.p0]       NOT AVAILABLE
[scipy-0.17.1.p0]
[scipy-0.17.1.p0]     Running from scipy source directory.
[scipy-0.17.1.p0]     Traceback (most recent call last):
[scipy-0.17.1.p0]       File "<string>", line 1, in <module>
[scipy-0.17.1.p0]       File "/tmp/pip-lnNxdH-build/setup.py", line 265,
in <module>
[scipy-0.17.1.p0]         setup_package()
[scipy-0.17.1.p0]       File "/tmp/pip-lnNxdH-build/setup.py", line 262,
in setup_package
[scipy-0.17.1.p0]         setup(**metadata)
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/core.py", line
135, in setup
[scipy-0.17.1.p0]         config = configuration()
[scipy-0.17.1.p0]       File "/tmp/pip-lnNxdH-build/setup.py", line 182,
in configuration
[scipy-0.17.1.p0]         config.add_subpackage('scipy')
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py",
line 1003, in add_subpackage
[scipy-0.17.1.p0]         caller_level = 2)
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py",
line 972, in get_subpackage
[scipy-0.17.1.p0]         caller_level = caller_level + 1)
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py",
line 909, in _get_configuration_from_setup_py
[scipy-0.17.1.p0]         config = setup_module.configuration(*args)
[scipy-0.17.1.p0]       File "scipy/setup.py", line 15, in configuration
[scipy-0.17.1.p0]         config.add_subpackage('linalg')
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py",
line 1003, in add_subpackage
[scipy-0.17.1.p0]         caller_level = 2)
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py",
line 972, in get_subpackage
[scipy-0.17.1.p0]         caller_level = caller_level + 1)
[scipy-0.17.1.p0]       File "/usr/local/src/sage-
git/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py",
line 909, in _get_configuration_from_setup_py
[scipy-0.17.1.p0]         config = setup_module.configuration(*args)
[scipy-0.17.1.p0]       File "scipy/linalg/setup.py", line 20, in
configuration
[scipy-0.17.1.p0]         raise NotFoundError('no lapack/blas resources
found')
[scipy-0.17.1.p0]     numpy.distutils.system_info.NotFoundError: no
lapack/blas resources found
[scipy-0.17.1.p0]     Running setup.py install for scipy: finished with
status 'error'
[scipy-0.17.1.p0] Cleaning up...
[scipy-0.17.1.p0]   Removing source in /tmp/pip-lnNxdH-build
[scipy-0.17.1.p0] Command "/usr/local/src/sage-git/local/bin/python -u
-c "import setuptools, tokenize;__file__='/tmp/pip-lnNxdH-
build/setup.py';exec(compile(getattr(tokenize, 'open',
open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
install --record /tmp/pip-TjA2nI-record/install-record.txt --single-
version-externally-managed --compile" failed with error code 1 in /tmp
/pip-lnNxdH-build/
[scipy-0.17.1.p0] Exception information:
[scipy-0.17.1.p0] Traceback (most recent call last):
[scipy-0.17.1.p0]   File "/usr/local/src/sage-git/local/lib/python2.7
/site-packages/pip-8.1.2-py2.7.egg/pip/basecommand.py", line 215, in
main
[scipy-0.17.1.p0]     status = self.run(options, args)
[scipy-0.17.1.p0]   File "/usr/local/src/sage-git/local/lib/python2.7
/site-packages/pip-8.1.2-py2.7.egg/pip/commands/install.py", line 317,
in run
[scipy-0.17.1.p0]     prefix=options.prefix_path,
[scipy-0.17.1.p0]   File "/usr/local/src/sage-git/local/lib/python2.7
/site-packages/pip-8.1.2-py2.7.egg/pip/req/req_set.py", line 742, in
install
[scipy-0.17.1.p0]     **kwargs
[scipy-0.17.1.p0]   File "/usr/local/src/sage-git/local/lib/python2.7
/site-packages/pip-8.1.2-py2.7.egg/pip/req/req_install.py", line 880, in
install
[scipy-0.17.1.p0]     spinner=spinner,
[scipy-0.17.1.p0]   File "/usr/local/src/sage-git/local/lib/python2.7
/site-packages/pip-8.1.2-py2.7.egg/pip/utils/__init__.py", line 718, in
call_subprocess
[scipy-0.17.1.p0]     % (command_desc, proc.returncode, cwd))
[scipy-0.17.1.p0] InstallationError: Command "/usr/local/src/sage-
git/local/bin/python -u -c "import setuptools, tokenize;__file__='/tmp
/pip-lnNxdH-build/setup.py';exec(compile(getattr(tokenize, 'open',
open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
install --record /tmp/pip-TjA2nI-record/install-record.txt --single-
version-externally-managed --compile" failed with error code 1 in /tmp
/pip-lnNxdH-build/
[scipy-0.17.1.p0] Error installing scipy.
[scipy-0.17.1.p0]
[scipy-0.17.1.p0] real  0m2.854s
[scipy-0.17.1.p0] user  0m2.265s
[scipy-0.17.1.p0] sys   0m0.476s
[scipy-0.17.1.p0]
************************************************************************
[scipy-0.17.1.p0] Error installing package scipy-0.17.1.p0
[scipy-0.17.1.p0]
************************************************************************
[scipy-0.17.1.p0] Please email sage-devel
(http://groups.google.com/group/sage-devel)
[scipy-0.17.1.p0] explaining the problem and including the relevant part
of the log file
[scipy-0.17.1.p0]   /usr/local/src/sage-
git/logs/pkgs/scipy-0.17.1.p0.log
[scipy-0.17.1.p0] Describe your computer, operating system, etc.
[scipy-0.17.1.p0] If you want to try to fix the problem yourself,
*don't* just cd to
[scipy-0.17.1.p0] /usr/local/src/sage-
git/local/var/tmp/sage/build/scipy-0.17.1.p0 and type 'make' or whatever
is appropriate.
[scipy-0.17.1.p0] Instead, the following commands setup all environment
variables
[scipy-0.17.1.p0] correctly and load a subshell for you to debug the
error:
[scipy-0.17.1.p0]   (cd '/usr/local/src/sage-
git/local/var/tmp/sage/build/scipy-0.17.1.p0' && '/usr/local/src/sage-
git/sage' --sh)
[scipy-0.17.1.p0] When you are done debugging, you can type "exit" to
leave the subshell.
[scipy-0.17.1.p0]
************************************************************************
}}}

URL: https://trac.sagemath.org/22047
Reported by: jdemeyer
Ticket author(s): François Bissey
Reviewer(s): Jeroen Demeyer

build/pkgs/atlas/package-version.txt

@@ -1 +1 @@
-3.10.2.p2
+3.10.2.p3

build/pkgs/atlas/spkg-install

@@ -223,11 +223,11 @@ if 'SAGE_ATLAS_LIB' in os.environ:
 
     sys.exit(0)
 
-write_pc_file(['cblas', 'atlas'], 'cblas')
-write_pc_file(['f77blas', 'atlas'], 'blas')
-# The inclusion of cblas is not a mistake. ATLAS' lapack include
-# a custom version of clapack which depends on cblas.
-write_pc_file(['lapack', 'f77blas', 'cblas', 'atlas'], 'lapack')
+# Because blas, cblas and lapack libraries are properly linked
+# with no unknown symbols, no extra libraries needs to be given.
+write_pc_file(['cblas'], 'cblas')
+write_pc_file(['f77blas'], 'blas')
+write_pc_file(['lapack'], 'lapack')
 
 # add extra architectural defaults
 cp('src/ARCHS/*.tar.bz2', 'src/ATLAS/CONFIG/ARCHS/')